def test_get_contigs(self):
'''Test get_contigs'''
a = assembly.Assembly(os.path.join(data_dir, 'assembly_test_get_contigs.fasta'))
expected = {
'contig1': pyfastaq.sequences.Fasta('contig1', 'ACGT'),
'contig2': pyfastaq.sequences.Fasta('contig2', 'AAAA'),
}
self.assertEqual(expected, a.get_contigs())
def test_init_file_not_dir(self):
'''Test _init_file_not_dir'''
contigs_fasta = os.path.join(data_dir, 'assembly_test_init_contigs.fasta')
a = assembly.Assembly(contigs_fasta)
self.assertEqual(a.contigs_fasta, contigs_fasta)
self.assertIsNone(a.contigs_fastg)
self.assertIsNone(a.assembly_graph_fastg)
self.assertIsNone(a.spades_dir)
def test_circular_contigs_just_fasta(self):
'''Test circular_contigs when input is just fasta'''
a = assembly.Assembly(
os.path.join(data_dir,
'assembly_test_circular_contigs_only_contigs.fasta'),
'spades')
got = a.circular_contigs()
expected = set()
self.assertEqual(expected, got)
def test_circular_contigs_spades_pre_3_6_1(self):
'''Test circular_contigs with spades pre 3.6.1'''
a = assembly.Assembly(
os.path.join(data_dir,
'assembly_test_circular_contigs_spades_pre_3_6_1'),
'spades')
got = a.circular_contigs()
expected = {'NODE_1_length_5_cov_42.42_ID_1'}
self.assertEqual(expected, got)
def test_init_post_3_6_1_ok(self):
'''Test _init_post_3_6_1_ok'''
test_dir = os.path.join(data_dir, 'assembly_test_init_spades_post_3_6_1_ok')
a = assembly.Assembly(test_dir)
self.assertEqual(a.spades_dir, test_dir)
self.assertEqual(a.contigs_fasta, os.path.join(test_dir, 'contigs.fasta'))
self.assertEqual(a.assembly_graph_fastg, os.path.join(test_dir, 'assembly_graph.fastg'))
self.assertEqual(a.contigs_paths, os.path.join(test_dir, 'contigs.paths'))
self.assertIsNone(a.contigs_fastg)
def test_circular_contigs_spades_post_3_6_1(self):
'''Test circular_contigs with spades post 3.6.1'''
a = assembly.Assembly(os.path.join(data_dir, 'assembly_test_circular_contigs_spades_post_3_6_1'))
got = a.circular_contigs()
expected = {
'NODE_5_length_8134_cov_20.6513_ID_2269',
'NODE_6_length_6712_cov_6.68474_ID_2271',
'NODE_7_length_4806_cov_3.33747_ID_2273',
'NODE_8_length_4566_cov_19.8709_ID_2275',
}
self.assertEqual(expected, got)
def test_init_raises_error(self):
'''Test _init_raises_error'''
test_dirs = [
'assembly_test_init_no_fasta',
'assembly_test_init_spades_pre_3_6_1_no_fastg',
'assembly_test_init_spades_post_3_6_1_no_contigs_paths',
'assembly_test_init_spades_post_3_6_1_no_assembly_graph',
'assembly_test_init_spades_post_3_6_1_no_assembly_graph_or_contig_paths',
]
for test_dir in test_dirs:
with self.assertRaises(assembly.Error):
a = assembly.Assembly(os.path.join(data_dir, test_dir))